Input configuration for GATK4-gCNV workflow on Terra

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Seunghun Han

• September 15, 2021 16:35

Hi,

I'm trying to run cnv_germline_cohort_worflow in https://app.terra.bio/#workspaces/help-gatk/Germline-CNVs-GATK4/workflows workspace on my two cohorts, one in hg19 and another in hg38, and the input configuration preset in the workflow is only for running tutorial on chromosome 20, X, and Y in hg19, and the dashboard refers to GATK documentations for correct configuration. I have carefully read 
this tutorial (https://gatk.broadinstitute.org/hc/en-us/articles/360035531152) and could learn what to use for some of the inputs, but there are still some inputs which require genome build specific files such as "contig_ploidy_priors" , "intervals", "mappability_track_bed /idx" , "segmental_duplication_track_bed/idx" , and some blacklist intervals that I have no clue where to get. 

Is there an established Terra input configuration/resources for running the workflow on hg19 and hg38 germline WES dataset? 

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  Samantha (she/her)

  • September 17, 2021 17:57

  Hi Seunghun Han,

  Thanks for writing in. We'll take a look at your question and get back to you as soon as we can.

  Best,

  Samantha

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  Seunghun Han

  • September 21, 2021 13:48

  Hi Samantha (she/her),
  
  Is there any update on this? 

  thanks,
  Seunghun 

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  Samantha (she/her)

  • September 21, 2021 20:09

  Hi Seunghun Han,

  The contig_ploidy_priors and intervals inputs are something you need to generate (with with WES data you'll need to start with the list of targets provided by the capture kit manufacturer). The instructions on their format and how to generate them can be found in the tutorial article you linked and this article.

  The  mappability_track_bed and segmental_duplication_track_bed files were in a private bucket, but they should now be in gs://gatk-best-practices/cnv-germline-pipeline.

   

  Best,

  Samantha

   

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  Seunghun Han

  • September 22, 2021 17:02

  Thanks a lot!!! This is exactly what I need. 

  Best,
  Seunghun

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  mariesmith

  • November 29, 2022 10:15

  Hi,

  I am not able to find those files for hg38 in the provided bucket gs://gatk-best-practices/cnv-germline-pipeline nor in https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0.

  Could you please tell me where I can find them?

  Thanks in advance!

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